src/jalview/gui/Jalview2XML.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 \r
  22 import jalview.schemes.*;\r
  23 \r
  24 import jalview.gui.*;\r
  25 \r
  26 import java.io.*;\r
  27 \r
  28 import java.net.*;\r
  29 \r
  30 import java.util.*;\r
  31 \r
  32 import java.util.jar.*;\r
  33 \r
  34 import javax.swing.*;\r
  35 \r
  36 import org.exolab.castor.xml.*;\r
  37 \r
  38 import jalview.schemabinding.version2.*;\r
  39 \r
  40 \r
  41 \r
  42 \r
  43 /**\r
  44  * DOCUMENT ME!\r
  45  *\r
  46  * @author $author$\r
  47  * @version $Revision$\r
  48  */\r
  49 public class Jalview2XML\r
  50 {\r
  51     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  52     public void SaveState(File statefile)\r
  53     {\r
  54         long creation = System.currentTimeMillis();\r
  55         JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  56 \r
  57         if (frames == null)\r
  58         {\r
  59             return;\r
  60         }\r
  61 \r
  62         try\r
  63         {\r
  64             FileOutputStream fos = new FileOutputStream(statefile);\r
  65             JarOutputStream jout = new JarOutputStream(fos);\r
  66 \r
  67             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  68             ////////////////////////////////////////////////////\r
  69             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  70                         "UTF-8"));\r
  71 \r
  72             Vector shortNames = new Vector();\r
  73 \r
  74             //REVERSE ORDER\r
  75             for (int i = frames.length - 1; i > -1; i--)\r
  76             {\r
  77                 if (frames[i] instanceof AlignFrame)\r
  78                 {\r
  79                     AlignFrame af = (AlignFrame) frames[i];\r
  80 \r
  81                     String shortName = af.getTitle();\r
  82 \r
  83                     if (shortName.indexOf(File.separatorChar) > -1)\r
  84                     {\r
  85                         shortName = shortName.substring(shortName.lastIndexOf(\r
  86                                     File.separatorChar) + 1);\r
  87                     }\r
  88 \r
  89                     int count = 1;\r
  90 \r
  91                     while (shortNames.contains(shortName))\r
  92                     {\r
  93                         if (shortName.endsWith("_" + (count - 1)))\r
  94                         {\r
  95                             shortName = shortName.substring(0,\r
  96                                     shortName.lastIndexOf("_"));\r
  97                         }\r
  98 \r
  99                         shortName = shortName.concat("_" + count);\r
 100                         count++;\r
 101                     }\r
 102 \r
 103                     shortNames.addElement(shortName);\r
 104 \r
 105                     if (!shortName.endsWith(".xml"))\r
 106                     {\r
 107                         shortName = shortName + ".xml";\r
 108                     }\r
 109 \r
 110                     SaveState(af, creation, shortName, jout, out);\r
 111                 }\r
 112             }\r
 113 \r
 114             out.close();\r
 115             jout.close();\r
 116         }\r
 117         catch (Exception ex)\r
 118         {\r
 119             ex.printStackTrace();\r
 120         }\r
 121     }\r
 122 \r
 123     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 124     public void SaveAlignment(AlignFrame af, String jarFile,\r
 125         String fileName)\r
 126     {\r
 127         try\r
 128         {\r
 129             FileOutputStream fos = new FileOutputStream(jarFile);\r
 130             JarOutputStream jout = new JarOutputStream(fos);\r
 131 \r
 132             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 133             ////////////////////////////////////////////////////\r
 134             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 135                         "UTF-8"));\r
 136 \r
 137             SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 138             out.close();\r
 139             jout.close();\r
 140         }\r
 141         catch (Exception ex)\r
 142         {\r
 143           ex.printStackTrace();\r
 144         }\r
 145     }\r
 146 \r
 147     /**\r
 148      * DOCUMENT ME!\r
 149      *\r
 150      * @param af DOCUMENT ME!\r
 151      * @param timeStamp DOCUMENT ME!\r
 152      * @param fileName DOCUMENT ME!\r
 153      * @param jout DOCUMENT ME!\r
 154      * @param out DOCUMENT ME!\r
 155      */\r
 156     public void SaveState(AlignFrame af, long timeStamp,\r
 157         String fileName, JarOutputStream jout, PrintWriter out)\r
 158     {\r
 159         Vector seqids = new Vector();\r
 160         Vector userColours = new Vector();\r
 161 \r
 162         AlignViewport av = af.viewport;\r
 163 \r
 164         JalviewModel object = new JalviewModel();\r
 165         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
 166 \r
 167         object.setCreationDate(new java.util.Date(timeStamp));\r
 168         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 169 \r
 170         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 171 \r
 172         SequenceSet vamsasSet = new SequenceSet();\r
 173         Sequence vamsasSeq;\r
 174         JalviewModelSequence jms = new JalviewModelSequence();\r
 175 \r
 176         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 177 \r
 178         JSeq jseq;\r
 179 \r
 180         //SAVE SEQUENCES\r
 181         int id = 0;\r
 182 \r
 183         for (int i = 0; i < jal.getHeight(); i++)\r
 184         {\r
 185             seqids.add(jal.getSequenceAt(i));\r
 186 \r
 187             vamsasSeq = new Sequence();\r
 188             vamsasSeq.setId(id + "");\r
 189             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 190             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 191             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 192 \r
 193             jseq = new JSeq();\r
 194             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 195             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 196 \r
 197             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 198 \r
 199             jseq.setId(id);\r
 200 \r
 201             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
 202             {\r
 203               jalview.datamodel.SequenceFeature[] sf\r
 204                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 205               int index = 0;\r
 206               while(index < sf.length)\r
 207               {\r
 208                 Features features = new Features();\r
 209 \r
 210                 features.setBegin(sf[index].getBegin());\r
 211                 features.setEnd(sf[index].getEnd());\r
 212                 features.setDescription(sf[index].getDescription());\r
 213                 features.setStatus(sf[index].getStatus());\r
 214                 features.setType(sf[index].getType());\r
 215                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
 216                 jseq.addFeatures(features);\r
 217                 index ++;\r
 218               }\r
 219             }\r
 220 \r
 221             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 222             {\r
 223               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 224               while(en.hasMoreElements())\r
 225               {\r
 226                 Pdbids pdb = new Pdbids();\r
 227                 jalview.datamodel.PDBEntry entry\r
 228                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 229 \r
 230                 pdb.setId(entry.getId());\r
 231                 pdb.setType(entry.getType());\r
 232 \r
 233                 if(entry.getProperty()!=null)\r
 234                 {\r
 235                   PdbentryItem item = new PdbentryItem();\r
 236                   Hashtable properties = entry.getProperty();\r
 237                   Enumeration en2 = properties.keys();\r
 238                   while(en2.hasMoreElements())\r
 239                   {\r
 240                     Property prop = new Property();\r
 241                     String key = en2.nextElement().toString();\r
 242                     prop.setName(key);\r
 243                     prop.setValue( properties.get(key).toString() );\r
 244                     item.addProperty(prop);\r
 245                   }\r
 246                   pdb.addPdbentryItem(item);\r
 247                 }\r
 248 \r
 249                 jseq.addPdbids(pdb);\r
 250               }\r
 251             }\r
 252 \r
 253             jms.addJSeq(jseq);\r
 254             vamsasSet.addSequence(vamsasSeq);\r
 255             id++;\r
 256         }\r
 257 \r
 258         //SAVE TREES\r
 259         ///////////////////////////////////\r
 260         if (af.viewport.currentTree != null)\r
 261         {\r
 262           // FIND ANY ASSOCIATED TREES\r
 263           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 264           if (Desktop.desktop != null)\r
 265           {\r
 266             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 267 \r
 268             for (int t = 0; t < frames.length; t++)\r
 269             {\r
 270               if (frames[t] instanceof TreePanel)\r
 271               {\r
 272                 TreePanel tp = (TreePanel) frames[t];\r
 273 \r
 274                 if (tp.treeCanvas.av.alignment == jal)\r
 275                 {\r
 276                   Tree tree = new Tree();\r
 277                   tree.setTitle(tp.getTitle());\r
 278                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 279                   tree.setNewick(tp.getTree().toString());\r
 280                   tree.setThreshold(tp.treeCanvas.threshold);\r
 281 \r
 282                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 283                   tree.setFontName(tp.getTreeFont().getName());\r
 284                   tree.setFontSize(tp.getTreeFont().getSize());\r
 285                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 286                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 287 \r
 288                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 289                   tree.setShowDistances(tp.distanceMenu.getState());\r
 290 \r
 291                   tree.setHeight(tp.getHeight());\r
 292                   tree.setWidth(tp.getWidth());\r
 293                   tree.setXpos(tp.getX());\r
 294                   tree.setYpos(tp.getY());\r
 295 \r
 296                   jms.addTree(tree);\r
 297                 }\r
 298               }\r
 299             }\r
 300           }\r
 301         }\r
 302 \r
 303         //SAVE ANNOTATIONS\r
 304         if (jal.getAlignmentAnnotation() != null)\r
 305         {\r
 306             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 307 \r
 308             for (int i = 0; i < aa.length; i++)\r
 309             {\r
 310                 if (aa[i].label.equals("Quality") ||\r
 311                         aa[i].label.equals("Conservation") ||\r
 312                         aa[i].label.equals("Consensus"))\r
 313                 {\r
 314                     continue;\r
 315                 }\r
 316 \r
 317                 Annotation an = new Annotation();\r
 318                 an.setDescription(aa[i].description);\r
 319 \r
 320                 if(aa[i].sequenceRef!=null)\r
 321                  {\r
 322                    an.setSequenceRef(aa[i].sequenceRef.getName());\r
 323                  }\r
 324 \r
 325                 if(aa[i].graph>0)\r
 326                 {\r
 327                   an.setGraph(true);\r
 328                   an.setGraphType(aa[i].graph);\r
 329                   if(aa[i].getThreshold()!=null)\r
 330                   {\r
 331                     ThresholdLine line = new ThresholdLine();\r
 332                     line.setLabel(aa[i].getThreshold().label);\r
 333                     line.setValue(aa[i].getThreshold().value);\r
 334                     line.setColour(aa[i].getThreshold().colour.getRGB());\r
 335                     an.setThresholdLine(line);\r
 336                   }\r
 337                 }\r
 338                 else\r
 339                   an.setGraph(false);\r
 340 \r
 341                 an.setLabel(aa[i].label);\r
 342 \r
 343                 AnnotationElement ae;\r
 344 \r
 345                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 346                 {\r
 347                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 348                     {\r
 349                         continue;\r
 350                     }\r
 351 \r
 352                     ae = new AnnotationElement();\r
 353                     ae.setDescription(aa[i].annotations[a].description);\r
 354                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 355                     ae.setValue(aa[i].annotations[a].value);\r
 356                     ae.setPosition(a);\r
 357                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 358                         "");\r
 359                     an.addAnnotationElement(ae);\r
 360                 }\r
 361 \r
 362                 vamsasSet.addAnnotation(an);\r
 363             }\r
 364         }\r
 365 \r
 366         //SAVE GROUPS\r
 367         if (jal.getGroups() != null)\r
 368         {\r
 369             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 370 \r
 371             for (int i = 0; i < groups.length; i++)\r
 372             {\r
 373                 groups[i] = new JGroup();\r
 374 \r
 375                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 376                                                                                           .elementAt(i);\r
 377                 groups[i].setStart(sg.getStartRes());\r
 378                 groups[i].setEnd(sg.getEndRes());\r
 379                 groups[i].setName(sg.getName());\r
 380                 if(sg.cs!=null)\r
 381                 {\r
 382                   if (sg.cs.conservationApplied())\r
 383                   {\r
 384                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 385 \r
 386                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 387                     {\r
 388                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 389                           userColours,\r
 390                           jms));\r
 391                     }\r
 392                     else\r
 393                     {\r
 394                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 395                           cs));\r
 396                     }\r
 397                   }\r
 398                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
 399                   {\r
 400                     groups[i].setColour(\r
 401                         ColourSchemeProperty.getColourName(\r
 402                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
 403                   }\r
 404                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 405                   {\r
 406                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 407                         jms));\r
 408                   }\r
 409                   else\r
 410                   {\r
 411                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 412                         sg.cs));\r
 413                   }\r
 414 \r
 415                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 416                 }\r
 417 \r
 418                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 419                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 420                 groups[i].setDisplayText(sg.getDisplayText());\r
 421                 groups[i].setColourText(sg.getColourText());\r
 422 \r
 423                 for (int s = 0; s < sg.getSize(); s++)\r
 424                 {\r
 425                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 426                     int index = seqids.indexOf(seq);\r
 427                     groups[i].addSeq(index);\r
 428                 }\r
 429             }\r
 430 \r
 431             jms.setJGroup(groups);\r
 432         }\r
 433 \r
 434 \r
 435         ///////////SAVE VIEWPORT\r
 436         Viewport view = new Viewport();\r
 437         view.setTitle(af.getTitle());\r
 438         view.setXpos(af.getX());\r
 439         view.setYpos(af.getY());\r
 440         view.setWidth(af.getWidth());\r
 441         view.setHeight(af.getHeight());\r
 442         view.setStartRes(av.startRes);\r
 443         view.setStartSeq(av.startSeq);\r
 444 \r
 445         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 446         {\r
 447             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 448                     userColours, jms));\r
 449         }\r
 450         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
 451         {\r
 452            jalview.schemes.AnnotationColourGradient acg\r
 453               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
 454 \r
 455             AnnotationColours ac = new AnnotationColours();\r
 456             ac.setAboveThreshold(acg.getAboveThreshold());\r
 457             ac.setThreshold(acg.getAnnotationThreshold());\r
 458             ac.setAnnotation(acg.getAnnotation());\r
 459             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
 460               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
 461                     userColours, jms));\r
 462             else\r
 463               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
 464 \r
 465             ac.setMaxColour(acg.getMaxColour().getRGB());\r
 466             ac.setMinColour(acg.getMinColour().getRGB());\r
 467             view.setAnnotationColours(ac);\r
 468             view.setBgColour("AnnotationColourGradient");\r
 469         }\r
 470         else\r
 471         {\r
 472             view.setBgColour(ColourSchemeProperty.getColourName(\r
 473                     av.getGlobalColourScheme()));\r
 474         }\r
 475 \r
 476         ColourSchemeI cs = av.getGlobalColourScheme();\r
 477 \r
 478         if(cs!=null)\r
 479         {\r
 480           if (cs.conservationApplied())\r
 481           {\r
 482             view.setConsThreshold(cs.getConservationInc());\r
 483             if (cs instanceof jalview.schemes.UserColourScheme)\r
 484               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 485           }\r
 486 \r
 487           if (cs instanceof ResidueColourScheme)\r
 488           {\r
 489             view.setPidThreshold(cs.getThreshold());\r
 490           }\r
 491         }\r
 492 \r
 493         view.setConservationSelected(av.getConservationSelected());\r
 494         view.setPidSelected(av.getAbovePIDThreshold());\r
 495         view.setFontName(av.font.getName());\r
 496         view.setFontSize(av.font.getSize());\r
 497         view.setFontStyle(av.font.getStyle());\r
 498         view.setRenderGaps(av.renderGaps);\r
 499         view.setShowAnnotation(av.getShowAnnotation());\r
 500         view.setShowBoxes(av.getShowBoxes());\r
 501         view.setShowColourText(av.getColourText());\r
 502         view.setShowConservation(av.showConservation);\r
 503         view.setShowFullId(av.getShowJVSuffix());\r
 504         view.setShowIdentity(av.showIdentity);\r
 505         view.setShowQuality(av.showQuality);\r
 506         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 507         view.setShowText(av.getShowText());\r
 508         view.setWrapAlignment(av.getWrapAlignment());\r
 509 \r
 510         if(av.featuresDisplayed!=null)\r
 511         {\r
 512           jalview.schemabinding.version2.FeatureSettings fs\r
 513               = new jalview.schemabinding.version2.FeatureSettings();\r
 514 \r
 515           String [] renderOrder =\r
 516               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
 517           for(int ro=0; ro<renderOrder.length; ro++)\r
 518           {\r
 519             Setting setting = new Setting();\r
 520             setting.setType(renderOrder[ro]);\r
 521             setting.setColour(\r
 522                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
 523                 );\r
 524 \r
 525             setting.setDisplay(\r
 526                 av.featuresDisplayed.containsKey(renderOrder[ro])\r
 527                 );\r
 528 \r
 529             fs.addSetting(setting);\r
 530 \r
 531           }\r
 532           jms.setFeatureSettings(fs);\r
 533 \r
 534         }\r
 535 \r
 536         jms.addViewport(view);\r
 537 \r
 538 \r
 539         object.setJalviewModelSequence(jms);\r
 540         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 541 \r
 542         try\r
 543         {\r
 544             if (!fileName.endsWith(".xml"))\r
 545             {\r
 546                 fileName = fileName + ".xml";\r
 547             }\r
 548 \r
 549             JarEntry entry = new JarEntry(fileName);\r
 550             jout.putNextEntry(entry);\r
 551 \r
 552             object.marshal(out);\r
 553         }\r
 554         catch (Exception ex)\r
 555         {\r
 556             ex.printStackTrace();\r
 557         }\r
 558     }\r
 559 \r
 560     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 561         Vector userColours, JalviewModelSequence jms)\r
 562     {\r
 563         String id = null;\r
 564         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 565 \r
 566         if (!userColours.contains(ucs))\r
 567         {\r
 568             userColours.add(ucs);\r
 569 \r
 570             java.awt.Color[] colours = ucs.getColours();\r
 571             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 572             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 573 \r
 574             for (int i = 0; i < colours.length; i++)\r
 575             {\r
 576                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 577                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 578                 jbucs.addColour(col);\r
 579             }\r
 580 \r
 581             id = "ucs" + userColours.indexOf(ucs);\r
 582             uc.setId(id);\r
 583             uc.setUserColourScheme(jbucs);\r
 584             jms.addUserColours(uc);\r
 585         }\r
 586 \r
 587         return id;\r
 588     }\r
 589 \r
 590    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 591         JalviewModelSequence jms, String id)\r
 592     {\r
 593         UserColours[] uc = jms.getUserColours();\r
 594         UserColours colours = null;\r
 595 \r
 596         for (int i = 0; i < uc.length; i++)\r
 597         {\r
 598             if (uc[i].getId().equals(id))\r
 599             {\r
 600                 colours = uc[i];\r
 601 \r
 602                 break;\r
 603             }\r
 604         }\r
 605 \r
 606         int csize = colours.getUserColourScheme().getColourCount();\r
 607         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 608 \r
 609         for (int i = 0; i < csize; i++)\r
 610         {\r
 611             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 612                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 613         }\r
 614 \r
 615         return new jalview.schemes.UserColourScheme(newColours);\r
 616     }\r
 617 \r
 618     /**\r
 619      * DOCUMENT ME!\r
 620      *\r
 621      * @param file DOCUMENT ME!\r
 622      */\r
 623     public AlignFrame LoadJalviewAlign(String file)\r
 624     {\r
 625 \r
 626         jalview.gui.AlignFrame af = null;\r
 627 \r
 628         try\r
 629         {\r
 630             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 631             URL url = null;\r
 632 \r
 633             if (file.startsWith("http://"))\r
 634             {\r
 635                 url = new URL(file);\r
 636             }\r
 637 \r
 638             JarInputStream jin = null;\r
 639             JarEntry jarentry = null;\r
 640             int entryCount = 1;\r
 641 \r
 642             do\r
 643             {\r
 644                 if (url != null)\r
 645                 {\r
 646                     jin = new JarInputStream(url.openStream());\r
 647                 }\r
 648                 else\r
 649                 {\r
 650                     jin = new JarInputStream(new FileInputStream(file));\r
 651                 }\r
 652 \r
 653                 for (int i = 0; i < entryCount; i++)\r
 654                 {\r
 655                     jarentry = jin.getNextJarEntry();\r
 656 \r
 657                   }\r
 658 \r
 659 \r
 660                   class NoDescIDResolver implements IDResolver\r
 661                   {\r
 662                     public Object resolve(String idref)\r
 663                     {\r
 664                       System.out.println(idref+" used");\r
 665                       return null;\r
 666                     }\r
 667                   }\r
 668 \r
 669 \r
 670                 if (jarentry != null)\r
 671                 {\r
 672                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 673                     JalviewModel object = new JalviewModel();\r
 674 \r
 675                     Unmarshaller unmar = new Unmarshaller(object);\r
 676                     unmar.setValidation(false);\r
 677                     object = (JalviewModel) unmar.unmarshal( in );\r
 678 \r
 679                     af = LoadFromObject(object);\r
 680                     entryCount++;\r
 681                 }\r
 682             }\r
 683             while (jarentry != null);\r
 684         }\r
 685         catch(java.net.UnknownHostException ex)\r
 686         {\r
 687           ex.printStackTrace();\r
 688           System.err.println("Couldn't locate Jalview XML file : " +\r
 689               ex + "\n");\r
 690            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 691                                     "Couldn't locate " + file,\r
 692                                     "URL not found",\r
 693                                     JOptionPane.WARNING_MESSAGE);\r
 694 \r
 695         }\r
 696         catch (Exception ex)\r
 697         {\r
 698           //Is Version 1 Jar file?\r
 699           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 700 \r
 701           if(af!=null)\r
 702           {\r
 703             System.out.println("Successfuly loaded archive file");\r
 704             return af;\r
 705           }\r
 706           ex.printStackTrace();\r
 707             System.err.println("Exception whilst loading jalview XML file : " +\r
 708                 ex + "\n");\r
 709              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 710                                       "Error loading  " + file,\r
 711                                       "Error loading Jalview file",\r
 712                                       JOptionPane.WARNING_MESSAGE);\r
 713 \r
 714         }\r
 715 \r
 716         return af;\r
 717     }\r
 718 \r
 719     AlignFrame LoadFromObject(JalviewModel object)\r
 720     {\r
 721         Vector seqids = new Vector();\r
 722         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 723         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 724 \r
 725         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 726 \r
 727         //////////////////////////////////\r
 728         //LOAD SEQUENCES\r
 729         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 730         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 731         for (int i = 0; i < vamsasSeq.length; i++)\r
 732         {\r
 733             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 734                     vamsasSeq[i].getSequence());\r
 735             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 736 \r
 737             jseqs[i].setStart(JSEQ[i].getStart());\r
 738             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 739             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 740             seqids.add(jseqs[i]);\r
 741         }\r
 742 \r
 743         ///SequenceFeatures are added to the DatasetSequence,\r
 744         // so we must create the dataset before loading features\r
 745         /////////////////////////////////\r
 746         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 747         al.setDataset(null);\r
 748         /////////////////////////////////\r
 749 \r
 750         for (int i = 0; i < vamsasSeq.length; i++)\r
 751         {\r
 752           if (JSEQ[i].getFeaturesCount() > 0)\r
 753           {\r
 754             Features[] features = JSEQ[i].getFeatures();\r
 755             for (int f = 0; f < features.length; f++)\r
 756             {\r
 757               jalview.datamodel.SequenceFeature sf\r
 758                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 759                   features[f].getDescription(), features[f].getStatus(),\r
 760                   features[f].getBegin(), features[f].getEnd(),\r
 761                   features[f].getFeatureGroup());\r
 762 \r
 763               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 764             }\r
 765           }\r
 766           if (JSEQ[i].getPdbidsCount() > 0)\r
 767           {\r
 768             Pdbids[] ids = JSEQ[i].getPdbids();\r
 769             for (int p = 0; p < ids.length; p++)\r
 770             {\r
 771               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 772               entry.setId(ids[p].getId());\r
 773               entry.setType(ids[p].getType());\r
 774               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 775             }\r
 776 \r
 777           }\r
 778         }\r
 779 \r
 780          /////////////////////////////////\r
 781         //////////////////////////////////\r
 782         //LOAD ANNOTATIONS\r
 783         if (vamsasSet.getAnnotation() != null)\r
 784         {\r
 785             Annotation[] an = vamsasSet.getAnnotation();\r
 786 \r
 787             for (int i = 0; i < an.length; i++)\r
 788             {\r
 789                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 790                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 791 \r
 792                 for (int aa = 0; aa < ae.length; aa++)\r
 793                 {\r
 794                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 795                             ae[aa].getDescription(),\r
 796                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
 797                             ae[aa].getValue());\r
 798                 }\r
 799 \r
 800                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 801 \r
 802                 if (an[i].getGraph())\r
 803                 {\r
 804                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 805                       an[i].getDescription(), anot, 0, 0,\r
 806                       an[i].getGraphType());\r
 807 \r
 808                   if (an[i].getThresholdLine() != null)\r
 809                   {\r
 810                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
 811                                   an[i].getThresholdLine().getValue(),\r
 812                                   an[i].getThresholdLine().getLabel(),\r
 813                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
 814                              );\r
 815 \r
 816                   }\r
 817 \r
 818                 }\r
 819                 else\r
 820                 {\r
 821                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 822                             an[i].getDescription(), anot);\r
 823                 }\r
 824 \r
 825                 if(an[i].getSequenceRef()!=null)\r
 826                 {\r
 827                   jaa.createSequenceMapping(\r
 828                       al.findName(an[i].getSequenceRef()), 1\r
 829                       );\r
 830                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
 831                 }\r
 832 \r
 833                 al.addAnnotation(jaa);\r
 834             }\r
 835         }\r
 836 \r
 837 \r
 838         /////////////////////////////////\r
 839         // LOAD VIEWPORT\r
 840         Viewport[] views = jms.getViewport();\r
 841         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 842 \r
 843         AlignFrame af = new AlignFrame(al);\r
 844 \r
 845 \r
 846         //  af.changeColour() );\r
 847         /////////////////////////\r
 848         //LOAD GROUPS\r
 849         if (jms.getJGroupCount() > 0)\r
 850         {\r
 851             JGroup[] groups = jms.getJGroup();\r
 852 \r
 853             for (int i = 0; i < groups.length; i++)\r
 854             {\r
 855                 ColourSchemeI cs = null;\r
 856 \r
 857                 if (groups[i].getColour() != null)\r
 858                 {\r
 859                     if (groups[i].getColour().startsWith("ucs"))\r
 860                     {\r
 861                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 862                     }\r
 863                     else\r
 864                     {\r
 865                         cs = ColourSchemeProperty.getColour(al,\r
 866                                 groups[i].getColour());\r
 867                     }\r
 868 \r
 869                     if(cs!=null)\r
 870                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
 871                 }\r
 872 \r
 873                 Vector seqs = new Vector();\r
 874                 int[] ids = groups[i].getSeq();\r
 875 \r
 876                 for (int s = 0; s < ids.length; s++)\r
 877                 {\r
 878                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 879                             ids[s]));\r
 880                 }\r
 881 \r
 882                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 883                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 884                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 885                         groups[i].getStart(), groups[i].getEnd());\r
 886 \r
 887                 sg.setOutlineColour(new java.awt.Color(\r
 888                         groups[i].getOutlineColour()));\r
 889 \r
 890                 if (groups[i].getConsThreshold() != 0)\r
 891                 {\r
 892                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 893                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 894                             sg.getWidth() - 1);\r
 895                     c.calculate();\r
 896                     c.verdict(false, 25);\r
 897                     sg.cs.setConservation(c);\r
 898                 }\r
 899 \r
 900                 al.addGroup(sg);\r
 901             }\r
 902         }\r
 903 \r
 904 \r
 905 \r
 906         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 907             view.getHeight());\r
 908         af.viewport.setStartRes(view.getStartRes());\r
 909         af.viewport.setStartSeq(view.getStartSeq());\r
 910         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 911         af.viewport.showConservation = view.getShowConservation();\r
 912         af.viewport.showQuality = view.getShowQuality();\r
 913         af.viewport.showIdentity = view.getShowIdentity();\r
 914         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 915         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 916         af.viewport.setColourText(view.getShowColourText());\r
 917         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 918         af.viewport.setConservationSelected(view.getConservationSelected());\r
 919         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 920 \r
 921         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 922         af.seqLimits.setSelected(view.getShowFullId());\r
 923 \r
 924         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 925                 view.getFontStyle(), view.getFontSize()));\r
 926         af.alignPanel.fontChanged();\r
 927 \r
 928         af.viewport.setRenderGaps(view.getRenderGaps());\r
 929         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 930 \r
 931         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 932         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 933 \r
 934         if (view.getWrapAlignment())\r
 935         {\r
 936             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 937         }\r
 938         else\r
 939         {\r
 940             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 941             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 942             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 943         }\r
 944 \r
 945         af.viewport.setShowBoxes(view.getShowBoxes());\r
 946         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 947         af.viewport.setShowText(view.getShowText());\r
 948         af.viewTextMenuItem.setSelected(view.getShowText());\r
 949 \r
 950         ColourSchemeI cs = null;\r
 951 \r
 952         if (view.getBgColour() != null)\r
 953         {\r
 954             if (view.getBgColour().startsWith("ucs"))\r
 955             {\r
 956                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 957             }\r
 958             else if(view.getBgColour().startsWith("Annotation"))\r
 959             {\r
 960               //int find annotation\r
 961               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
 962               {\r
 963                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
 964                     equals(view.getAnnotationColours().getAnnotation()))\r
 965                 {\r
 966                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
 967                       getThreshold() == null)\r
 968                   {\r
 969                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
 970                         setThreshold(\r
 971                             new jalview.datamodel.GraphLine(\r
 972                                 view.getAnnotationColours().getThreshold(),\r
 973                                 "Threshold", java.awt.Color.black)\r
 974 \r
 975                         );\r
 976                   }\r
 977 \r
 978 \r
 979                   if (view.getAnnotationColours().getColourScheme().equals(\r
 980                       "None"))\r
 981                   {\r
 982                     cs = new AnnotationColourGradient(\r
 983                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
 984                         new java.awt.Color(view.getAnnotationColours().\r
 985                                            getMinColour()),\r
 986                         new java.awt.Color(view.getAnnotationColours().\r
 987                                            getMaxColour()),\r
 988                         view.getAnnotationColours().getAboveThreshold());\r
 989                   }\r
 990                   else if (view.getAnnotationColours().getColourScheme().\r
 991                            startsWith("ucs"))\r
 992                   {\r
 993                      cs = new AnnotationColourGradient(\r
 994                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
 995                          GetUserColourScheme(jms, view.getAnnotationColours().\r
 996                                                         getColourScheme()),\r
 997                          view.getAnnotationColours().getAboveThreshold()\r
 998                          );\r
 999                    }\r
1000                    else\r
1001                    {\r
1002                      cs = new AnnotationColourGradient(\r
1003                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1004                          ColourSchemeProperty.getColour(al,\r
1005                          view.getAnnotationColours().getColourScheme()),\r
1006                          view.getAnnotationColours().getAboveThreshold()\r
1007                          );\r
1008                    }\r
1009 \r
1010                   // Also use these settings for all the groups\r
1011                   if (al.getGroups() != null)\r
1012                     for (int g = 0; g < al.getGroups().size(); g++)\r
1013                     {\r
1014                       jalview.datamodel.SequenceGroup sg\r
1015                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1016 \r
1017                       if(sg.cs == null)\r
1018                         continue;\r
1019 \r
1020 \r
1021                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1022                       {\r
1023                         sg.cs = new AnnotationColourGradient(\r
1024                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1025                             new java.awt.Color(view.getAnnotationColours().\r
1026                                                getMinColour()),\r
1027                             new java.awt.Color(view.getAnnotationColours().\r
1028                                                getMaxColour()),\r
1029                             view.getAnnotationColours().getAboveThreshold());\r
1030                       }\r
1031                       else*/\r
1032                       {\r
1033                         sg.cs = new AnnotationColourGradient(\r
1034                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1035                             sg.cs,\r
1036                             view.getAnnotationColours().getAboveThreshold()\r
1037                             );\r
1038                       }\r
1039 \r
1040                     }\r
1041 \r
1042 \r
1043                   break;\r
1044                 }\r
1045 \r
1046               }\r
1047             }\r
1048             else\r
1049             {\r
1050                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1051             }\r
1052 \r
1053             if(cs!=null)\r
1054             {\r
1055               cs.setThreshold(view.getPidThreshold(), true);\r
1056               cs.setConsensus(af.viewport.vconsensus);\r
1057             }\r
1058         }\r
1059 \r
1060         af.setColourSelected(view.getBgColour());\r
1061         af.viewport.setGlobalColourScheme(cs);\r
1062         af.viewport.setColourAppliesToAllGroups(false);\r
1063         af.changeColour(cs);\r
1064         if (view.getConservationSelected() && cs!=null)\r
1065         {\r
1066           cs.setConservationInc(view.getConsThreshold());\r
1067         }\r
1068 \r
1069         af.viewport.setColourAppliesToAllGroups(true);\r
1070 \r
1071         if (view.getShowSequenceFeatures())\r
1072         {\r
1073            af.viewport.showSequenceFeatures = true;\r
1074            af.showSeqFeatures.setSelected(true);\r
1075         }\r
1076 \r
1077         if(jms.getFeatureSettings()!=null)\r
1078         {\r
1079           af.viewport.featuresDisplayed = new Hashtable();\r
1080           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1081          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1082          {\r
1083            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1084 \r
1085            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1086                new java.awt.Color(setting.getColour()));\r
1087 \r
1088            renderOrder[fs] = setting.getType();\r
1089 \r
1090            if(setting.getDisplay())\r
1091              af.viewport.featuresDisplayed.put(\r
1092                  setting.getType(), new Integer(setting.getColour()));\r
1093          }\r
1094          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1095         }\r
1096 \r
1097 \r
1098         Desktop.addInternalFrame(af, view.getTitle(),\r
1099              view.getWidth(), view.getHeight());\r
1100 \r
1101         //LOAD TREES\r
1102         ///////////////////////////////////////\r
1103         if (jms.getTreeCount() > 0)\r
1104         {\r
1105             try\r
1106             {\r
1107                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1108                 {\r
1109 \r
1110                     Tree tree = jms.getTree(t);\r
1111 \r
1112                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1113                                 tree.getNewick()), tree.getTitle(),\r
1114                                 tree.getWidth(), tree.getHeight(),\r
1115                                 tree.getXpos(), tree.getYpos());\r
1116 \r
1117                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1118                     tp.fitToWindow_actionPerformed(null);\r
1119 \r
1120                     if(tree.getFontName()!=null)\r
1121                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1122                                           tree.getFontStyle(),\r
1123                                           tree.getFontSize()));\r
1124                     else\r
1125                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1126                                             view.getFontStyle(),\r
1127                                             tree.getFontSize()));\r
1128 \r
1129                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1130                     tp.showBootstrap(tree.getShowBootstrap());\r
1131                     tp.showDistances(tree.getShowDistances());\r
1132 \r
1133                     tp.treeCanvas.threshold = tree.getThreshold();\r
1134 \r
1135                     if (tree.getCurrentTree())\r
1136                       af.viewport.setCurrentTree(tp.getTree());\r
1137                 }\r
1138 \r
1139             }\r
1140             catch (Exception ex)\r
1141             {\r
1142                 ex.printStackTrace();\r
1143             }\r
1144 \r
1145         }\r
1146 \r
1147         return af;\r
1148     }\r
1149 }\r
1150 \r